User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.3k
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Italy
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@jotsetung
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5 days, 13 hours ago
Joined:
4 years, 1 month ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 258 results • page 1 of 26 • next >
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Comment: C: make TxDb from list of genes
... I agree with James. No need to create a new TxDb database. You could simply subset an EnsDb database to your list of input genes (even better if you have Ensembl IDs): assuming you have your Ensembl gene IDs in a variable called ensids: library(EnsDb.Hsapiens.v86) edb <- filter(EnsDb.Hsapiens.v ...
written 8 days ago by Johannes Rainer1.3k
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Answer: A: Pick coding vs non-coding from Ensembl data set
... You can simply filter the complete EnsDb database to contain only protein coding genes or all other genes (note: this includes miRNA genes, lincRNAs, pseudogenes, snoRNA, scaRNA, sRNA, scRNA, rRNA ...). > library(EnsDb.Hsapiens.v86) > ## Filter the EnsDb database for protein coding genes > ...
written 16 days ago by Johannes Rainer1.3k
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Comment: C: Ensembl plants at annotationHub?
... I've generated the EnsDb. You can get the file from here https://www.dropbox.com/sh/wglt28zlfzhjubs/AADzGqJ0zydKRmdqbOsH_Ru5a?dl=0 after unzipping you can simply load the sqlite file with edb <- EnsDb(<sqlite-file>)   ...
written 22 days ago by Johannes Rainer1.3k
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Comment: C: Ensembl plants at annotationHub?
... Lori, do you think it might be usefull to add also EnsDb for all species in ensemblgenomes to AnnotationHub (starting ev "only" with plants)?   ...
written 22 days ago by Johannes Rainer1.3k
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Answer: A: Ensembl plants at annotationHub?
... Dear Guido, while it is possible to create EnsDb databases also for ensemblgenomes (including plants, funghi etc) I did not do this on a regular basis and was also hesitant to add these to AnnotationHub because I was not sure how many users there will be for these. Just let me know which species ( ...
written 23 days ago by Johannes Rainer1.3k
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... Yes, looks like that. You could also specifically look in the package libary directory  (EnsDb.Hsapiens.v86/extdata) in the path where your library is (which you get with .libPaths() in R). Please let me know if re-installation solved the problem. ...
written 24 days ago by Johannes Rainer1.3k
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Comment: C: R failing to load genome files from EnsDb.Hsapiens.v86
... This is indeed strange. By default, when loading the EnsDb.Hsapiens.v86 all sqlite files in the package's extdata folder get bound and exported as a variable. Can you verify that your package contains such an sqlite file? > dir(system.file("extdata", package = "EnsDb.Hsapiens.v86")) [1] "EnsDb. ...
written 24 days ago by Johannes Rainer1.3k
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Job: Postdoctoral researcher in Computational Metabolomics
... Eurac Research is looking for a Postdoctoral researcher in Computational Metabolomics   The Institute for Biomedicine is seeking a highly motivated researcher to join the Computational Metabolomics team.   The Institute for Biomedicine is home to an international and interdisciplinary team of scie ...
metabolomics xcms job metabolism population written 26 days ago by Johannes Rainer1.3k
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Comment: C: mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus
... Got a reply from the Ensembl support: they are aware of this inconsistency but did not solve it so far. They are working on it, but it won't happen before the next release.   ...
written 6 weeks ago by Johannes Rainer1.3k
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Comment: C: mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus
... In the perl function that I'm using to create the EnsDbs I'm using the Ensembl Perl API and in fact calling is_circular on each chromosome (slice). Seems that even for chromosome MT this returns 0 (i.e. FALSE). I did contact the Ensembl support to ask for details on that. I'll keep you updated. ...
written 6 weeks ago by Johannes Rainer1.3k

Latest awards to Johannes Rainer

Scholar 6 weeks ago, created an answer that has been accepted. For A: biomaRt package problem
Popular Question 6 weeks ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 6 weeks ago, created a question with more than 1,000 views. For How to get from xcmsRaw to a xcmsSet
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Reading alignments above a mapq threshold from BAM files
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 3 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Popular Question 6 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Popular Question 6 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Scholar 17 months ago, created an answer that has been accepted. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Scholar 17 months ago, created an answer that has been accepted. For A: Programatically download correct genome wide annotation package for given organi
Scholar 17 months ago, created an answer that has been accepted. For A: Is it possible to get Ensembl gene descriptions with ensembldb?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 17 months ago, created a post with more than 5 votes. For A: How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
Appreciated 17 months ago, created a post with more than 5 votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Popular Question 17 months ago, created a question with more than 1,000 views. For Plot data from VCF using Gviz?
Popular Question 17 months ago, created a question with more than 1,000 views. For reactome.db: reactome IDs not mapped to pathway names
Guru 17 months ago, received more than 100 upvotes.
Voter 17 months ago, voted more than 100 times.
Scholar 17 months ago, created an answer that has been accepted. For A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
Scholar 18 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 18 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 19 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 20 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Scholar 20 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype

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